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Biochemical Genetics (v.48, #5-6)

Putative Recombination Events and Evolutionary History of Five Economically Important Viruses of Fruit Trees Based on Coat Protein-Encoding Gene Sequence Analysis by Moncef Boulila (pp. 357-375).

To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31β algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.

Keywords: Bioinformatics; Phylogeny; Recombination; Fruit viruses; Sequence; Coat protein gene

Analysis of Geographic and Pairwise Genetic Distances Among Sheep Populations by Wei Sun; Hong Chang; Kenji Tsunoda; Hassan Musa; Yuehui Ma; Weijun Guan (pp. 376-384).

This study assessed the usefulness of geographic and pairwise genetic distances in the characterization of five sheep populations using 15 microsatellite markers. The average F statistics across loci were F _IT = 0.523 ± 0.140, F _ST = 0.363 ± 0.131, and F _IS = 0.263 ± 0.092. The average heterozygosity was 0.716 ± 0.069, polymorphism information content was 0.691 ± 0.070, and effective number of alleles was 3.736 ± 0.998. Sheep populations clustered into group 1 (Hu and Tong breeds) and group 2 (small-tailed Han, Wadi, and Tan breeds). Reynolds’ distance varied from 0.0062 to 0.0499, and the range of gene flow (N _m) was 4.8834–40.0726 among the sheep populations. The results showed that the genetic structure of the five populations was not consistent with their genetic distances, and the population genetic divergence was not linearly related to geographic distance as indicated by a Mantel test (P = 0.7936).

Keywords: Geographic distance; Pairwise distance; Sheep population

Genetic Diversity and Phylogenetic Relationships of Two Closely Related Northeast China Vicia Species Revealed with RAPD and ISSR Markers by Ying Han; Hao-You Wang (pp. 385-401).

RAPD and ISSR analyses revealed genetic diversity and relationships among 11 populations of two closely related northeast China Vicia species, Vicia ramuliflora and V. unijuga. Both methods yielded similar and complementary results, showing high genetic diversity. Vicia ramuliflora had 100% polymorphic loci in both RAPD and ISSR, and V. unijuga had 100% polymorphic loci for RAPD and 98.96% for ISSR. Genetic differentiation was moderate among populations of each species. Genetic variation was distributed mainly within populations for the two species. The high level of gene flow was important for the allocation of genetic variation. The UPGMA dendrogram and principal coordinates analysis at the level of individuals and populations showed that V. ramuliflora and V. unijuga were more closely related than either of them was to the outgroup species, V. cracca. The small molecular variance of V. ramuliflora and V. unijuga supports the conclusion that these two species had a common ancestor.

Keywords: Phylogenetic relationships; RAPD; ISSR; Vicia ramuliflora ; Vicia unijuga ; Vicia cracca ; Genetic diversity

Demographic History and Population Structure of Blackfin Flounder (Glyptocephalus stelleri) in Japan Revealed by Mitochondrial Control Region Sequences by Yongshuang Xiao; Tianxiang Gao; Yan Zhang; Takashi Yanagimoto (pp. 402-417).

The demographic history and population genetic structure of the blackfin flounder (Glyptocephalus stelleri) along coastal regions of Japan were investigated. Genetic variation in DNA sequences was examined from the first hypervariable region of the mitochondrial DNA control region. A high level of haplotypic diversity (h = 0.99 ± 0.004) was detected, indicating a high level of intrapopulation genetic diversity. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. The demographic history of G. stelleri was examined using neutrality tests and mismatch distribution analysis, which also indicated a Pleistocene population expansion at about 124,100–413,400 years ago. Hierarchical molecular variance analysis and conventional population Fst comparisons revealed no significant genetic differentiation throughout the range examined.

Keywords: Glyptocephalus stelleri ; Control region; Genetic diversity; Demographic history; Genetic structure

High-Altitude Adaptation of Yak Based on Genetic Variants and Activity of Lactate Dehydrogenase-1 by Liangde Kuang; Yucai Zheng; Yaqiu Lin; Yaou Xu; Suyu Jin; Yuping Li; Feng Dong; Zhongyong Jiang (pp. 418-427).

This study investigates the molecular mechanism by which yaks (Bos grunniens) adapt to hypoxia based on lactate dehydrogenase (LDH). Three LDH1 variants of the yak were revealed in tissue extracts by electrophoresis, including LDH1-F, LDH1-M, and LDH1-S. Kinetic analysis using purified LDH1 variants showed that the yak LDH1-M variant exhibited a similar K _m (NADH) and the same mobility on a gel as bovine LDH1, and the LDH1-F variant showed significant differences in K _m values for NADH or pyruvate from the other two variants of yak LDH1 and bovine LDH1. Among the three muscles assayed, yak longissimus dorsi showed the highest LDH activity and the lowest malate dehydrogenase (MDH) activity; heart muscle was exactly the opposite. Our results suggest that the three LDH1 variants might play an important role in the adaptation to hypoxia.

Keywords: Yak; Lactate dehydrogenase; Genetic variants; Molecular adaptation

Utility of Spermidine in PCR Amplification of Stool Samples by Arizumi Kikuchi; Takahiro Sawamura; Naoto Kawase; Yasuhiro Kitajima; Toshiaki Yoshida; Osami Daimaru; Takeo Nakakita; Shinichi Itoh (pp. 428-432).

High MHC DQB Variation and Asymmetric Allelic Distribution in the Endangered Yangtze Finless Porpoise, Neophocaena phocaenoides asiaeorientalis by Hejun Du; Jinsong Zheng; Min Wu; Qingzhong Zhao; Ding Wang (pp. 433-449).

The endangered Yangtze finless porpoise is found in the middle and lower reaches of the Yangtze River and its adjoining big lakes. To explore the major histocompatibility complex (MHC) genetic diversity and allelic distribution patterns across its range, we investigated variation at DQB exon 2. From 76 porpoises, we identified 18 DQB sequences. The freshwater Yangtze populations had much higher allelic diversity than marine populations. Among these freshwater populations, the middle-reach population had higher allelic diversity than the lower-reach population. The high DQB diversity level, relative to that of a neutral mtDNA locus, suggests that balancing selection is acting at the DQB gene and that rapid evolution and local positive selection play critical roles in generating and retaining high MHC diversity in the freshwater population. As the balancing selection might be driven by environmental pathogens, we suggest that maintaining MHC variation should be a high priority in the conservation and management of this endangered population, especially as an ex situ conservation strategy.

Keywords: Yangtze finless porpoise; DQB; Genetic variation; Balancing selection; Conservation

Effect of the g.–723G→T Polymorphism in the Bovine Myogenic Factor 5 (Myf5) Gene Promoter Region on Gene Transcript Level in the Longissimus Dorsi Muscle and on Meat Traits of Polish Holstein-Friesian Cattle by Dagmara Robakowska-Hyżorek; Jolanta Oprządek; Beata Żelazowska; Rafał Olbromski; Lech Zwierzchowski (pp. 450-464).

Myogenic factor 5 (Myf5), a product of the Myf5 gene, belongs to the MRF family of basic helix-loop-helix transcription factors that regulate myogenesis. Their roles in muscle growth and development make their genes candidates for molecular markers of meat production in livestock, but nucleotide sequence polymorphism has not been thoroughly studied in MRF genes. We detected four single nucleotide polymorphisms (SNPs) within exon 1 of the Myf5 gene, encoding the NH-terminal transactivation domain of the Myf5 protein. Three of these mutations change the amino acid sequence. The distribution of these SNPs was highly skewed in cattle populations; most of the mutations were found in only a few or even single individuals. Of the nine SNPs found in the promoter region of Myf5, one (transversion g.–723G→T) was represented by all three genotypes distributed in the cattle populations studied. This polymorphism showed an influence on Myf5 gene expression in the longissimus dorsi muscle and was associated with sirloin weight and fat weight in sirloin in carcasses of Holstein-Friesian cattle.

Keywords: Cattle; Myf5 gene; Bovine; Polymorphism; Meat traits

Genetic Variation of the Peroxisome Proliferator-Activated Receptor α Gene (PPARA) in Chickens Bred for Different Purposes by J. Q. Zhang; H. Chen; Z. J. Sun; X. L. Liu; Y. Z. Qiang-Ba; Y. L. Gu (pp. 465-471).

Peroxisome proliferator-activated receptor α (PPARA) is involved in fatty acid oxidation by upregulating the expression of acyl-coenzyme A oxidase and carnitine palmitoyltransferase. In this study, PPARA gene variations in four chicken breeds (Guyuan, Wenchang, Tibetan, and Hisex) were detected by PCR-SSCP and DNA sequencing. The results indicated six genotypes (AA-EF). When compared with the PPARA reference sequence (GenBank accession no. AF163809), the nucleotide sequences of genotypes AA, BB, AB, and CC revealed silent mutations in the three Chinese breeds. The nucleotide sequences of genotypes DD and EF in Hisex showed several frame-shift mutations, implying variations involving five alleles of the PPARA gene in chicken breeds. In addition, the distribution of genotype frequency within the PPARA gene was significantly different in the four breeds studied, implying that this locus would probably be an effective marker in marker-assisted selection for layer, meat-and-egg, and broiler breeds.

Keywords: Chicken; Peroxisome proliferator-activated receptor α gene (PPARA); PCR-SSCP; Genetic variation

Comparative Genetic Diversity of Wild and Captive Populations of the Bare-Faced Curassow (Crax fasciolata) Based on Cross-Species Microsatellite Markers: Implications for Conservation and Management by Evonnildo C. Gonçalves; Stephen F. Ferrari; Heitor B. Bastos; Anita Wajntal; Alexandre Aleixo; Maria Paula C. Schneider (pp. 472-479).

The bare-faced curassow (Crax fasciolata) is a large Neotropical bird that suffers anthropogenic pressure across much of its range. A captive population is maintained for conservation management, although there has been no genetic screening of stocks. Based on the six microsatellite markers developed for Crax globulosa, the genetic variability of C. fasciolata and possible differences between a wild and a captive population were investigated. Only three loci were polymorphic, with a total of 27 alleles. More than half of these alleles were private to the wild (n = 8) or captive (n = 7) populations. Significant deviations from Hardy–Weinberg equilibrium were restricted to the captive population. Despite the number of private alleles, genetic drift has probably promoted differentiation between populations. Our results indicate that wild C. fasciolata populations are genetically impoverished and structured, but species-specific microsatellite markers will be necessary for a more reliable assessment of the species’ genetic diversity.

Keywords: Bare-faced curassow; Crax fasciolata ; Population genetics; Microsatellites; Conservation

Cloning, Heterologous Expression, and Characterization of the Xylitol and l-Arabitol Dehydrogenase Genes, Texdh and Telad, from the Thermophilic Fungus Talaromyces emersonii by Sara Fernandes; Maria G. Tuohy; Patrick G. Murray (pp. 480-495).

The genes encoding xylitol dehydrogenase (Texdh) and l-arabitol dehydrogenase (Telad) are involved in the fungal pentose pathway and were isolated from the thermophilic fungus Talaromyces emersonii, expressed in Escherichia coli, and the products purified to homogeneity. TeXDH showed activity toward xylitol and d-sorbitol. TeLAD was active with l-arabitol, xylitol, and d-sorbitol. Phylogenetic analysis showed TeLAD has evolved from d-sorbitol dehydrogenase as a result of environmental adaptation. Substrate specificity studies indicate that TeXDH is likely to have evolved from the more broadly acting TeLAD. Texdh and Telad expression was inducible by the same carbon sources responsible for induction of genes involved in biomass degradation, suggesting for the first time a coordinated regulatory control mechanism for expression of genes encoding extracellular hydrolases and intracellular metabolic genes in the pentose utilization pathways of T. emersonii. These data also suggest that TeXDH and TeLAD may be valuable in the production of xylitol, l-arabitol, and ethanol from renewable resources rich in pentose sugars.

Keywords: Talaromyces emersonii ; Xylitol dehydrogenase; l-arabitol dehydrogenase

Association Analysis of the RET Proto-Oncogene with Hirschsprung Disease in the Han Chinese Population of Southeastern China by Cui-Ping Liu; Qian-Qian Tang; Jin-Tu Lou; Chun-Fen Luo; Xue-Wu Zhou; Dong-Mei Li; Fei Chen; Xiang Li; Ji-Cheng Li (pp. 496-503).

Hirschsprung disease (HSCR) is a complex congenital disorder characterized by intestinal obstructions caused by the absence of the intestinal ganglion cells of the nerve plexuses in variable lengths of the digestive tract. This study investigated a possible role of the RET proto-oncogene in sporadic HSCR patients in the Han Chinese population. Our results indicated that rs1800858, rs1800860, rs1800863, and rs2075912, located in exons 2, 7, 15, and intron 19 of RET, are strongly associated with the disease (P < 0.01), with rs1800860 and rs1800863 playing a protective role in the pathogenesis of HSCR in the Chinese population. We also showed that the haplotype consisting of four SNPs is significantly associated with HSCR. We did not find a significant difference in the CA-repeat in intron 5 of RET between cases and controls. Our study provided further evidence that the RET gene is involved in the susceptibility to HSCR in the Han Chinese population.

Keywords: Hirschsprung disease; RET proto-oncogene; Single nucleotide polymorphism; Haplotype; Linkage disequilibrium

Cloning and Characterization of p8 Homolog cDNA in the Atlantic Halibut (Hippoglossus hippoglossus) by Jia-Qing Wang; Lin-Chun Li; Sheng-Guo Lin; Zhi-Ping Wang (pp. 504-515).

The p8 gene encodes a transcription factor known to modulate cell growth, division, and apoptosis and influences gene expression. In this study, an Atlantic halibut (Hippoglossus hippoglossus) homolog of the p8 gene was cloned, sequenced, and characterized. The full-length p8 cDNA consists of 601 bp and encodes 76 amino acids with a molecular mass of 9 kD. The bHLH region is well conserved between Atlantic halibut and other animals. Analysis by RT-PCR showed that the p8 transcript is constitutively expressed in 9 of the 12 tissues tested: pancreas, intestine, stomach, gill, head kidney, heart, liver, ovary, and spleen. A predicted microRNA target site was found in the 3′UTR of Atlantic halibut p8 mRNA. We speculate that the target site may pair to microRNA molecules because the target site resides in a big loop, a space large enough for the binding of microRNA molecules.

Keywords: Atlantic halibut; p8 gene; mRNA tissue distribution; miRNA targets; Phylogenetic analysis

Insertion/Deletion Polymorphism and Serum Activity of the Angiotensin-Converting Enzyme in Turkish Patients with Obstructive Sleep Apnea Syndrome by Candan Ogus; Serap Ket; Turker Bilgen; Ibrahim Keser; Aykut Cilli; Ayse Yesim Gocmen; Ozgur Tosun; Saadet Gumuslu (pp. 516-523).

This study determined the allelic frequency and genotypic distribution of an angiotensin-converting enzyme (ACE) polymorphism and serum ACE activity in Turkish patients with obstructive sleep apnea syndrome (OSAS). A colorimetric assay measured serum ACE activity in 73 of 97 subjects. Frequencies for II, ID, and DD genotypes were 19.6, 53.6, and 26.8% in the OSAS group and 15, 38, and 47% in the control group, respectively (P = 0.02). The I allele frequency was higher in the OSAS group than in the healthy control group (P = 0.02). Carrying the I allele (II or ID genotypes) increased OSAS risk 2.41 times in the Turkish population. Mean ACE activity was significantly lower in patients with the II genotype than in the DD genotype (P = 0.011), and ACE activity was significantly lower in patients with severe OSAS than in those with mild OSAS (P = 0.006). Our results suggest that II and ID genotypes of the ACE gene increase the risk of developing OSAS in the Turkish population.

Keywords: ACE I/D polymorphism; Angiotensin-converting enzyme (ACE) serum activity; Obstructive sleep apnea syndrome (OSAS); Turkish population

Molecular Characterization of Fusarium oxysporum f. melongenae by ISSR and RAPD Markers on Eggplant by Ö. Baysal; M. Siragusa; E. Gümrükcü; S. Zengin; F. Carimi; M. Sajeva; Jaime A. Teixeira da Silva (pp. 524-537).

Fusarium oxysporum f. melongenae is a major soil-borne pathogen of eggplant (Solanum melongena). ISSR and RAPD markers were used to characterize Fusarium oxysporum f. melongenae isolates collected from eggplant fields in southern Turkey. Those isolates were not pathogenic to tomato. Pathogens were identified by their morphology, and their identity was confirmed by PCR amplification using the specific primer PF02-3. The isolates were classified into groups on the basis of ISSR and RAPD fingerprints, which showed a level of genetic specificity and diversity not previously identified in Fusarium oxysporum f. melongenae, suggesting that genetic differences are related to the pathogen in the Mediterranean region. The primers selected to characterize Fusarium oxysporum f. melongenae may be used to determine genetic differences and pathogen virulence. This study is the first to characterize eggplant F. oxysporum species using ISSR and RAPD.

Keywords: Fusarium; Molecular marker; Virulence; Genetic difference

Identification of a QTL for Adipocyte Volume and of Shared Genetic Effects with Aspartate Aminotransferase by Tanushree Bose; V. Saroja Voruganti; M. Elizabeth Tejero; J. Michael Proffit; Laura A. Cox; John L. VandeBerg; Michael C. Mahaney; Jeffrey Rogers; Jeanne H. Freeland-Graves; Shelley A. Cole; Anthony G. Comuzzie (pp. 538-547).

Plasma levels of aspartate aminotransferase (AST), a liver enzyme, are elevated in patients with visceral obesity. This study examined whether adipocyte volume is under the influence of genetic factors and evaluated its genetic correlations with AST. Fasting plasma levels of 344 pedigreed baboons from the Southwest National Primate Research Center in San Antonio, TX, USA, were assayed for AST. Adipocyte volume was measured using biopsies of omental adipose tissue. Adipocyte volume, body weight, and plasma AST were heritable. Genetic correlations between the measured adiposity-related phenotypes and AST were significant. A quantitative trait locus (LOD score 3.2) for adipocyte volume was identified on the baboon homolog of human chromosome 6 near marker D6S1028. These results suggest that omental adipocyte volume is under genetic regulation and that shared genetic factors influence adiposity-associated traits and AST.

Keywords: Nonalcoholic fatty liver disease; Obesity; Adipocyte size; Genome scan; QTL; Aspartate aminotransferase

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Biochemical Genetics (v.48, #5-6)

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Biochemical Genetics (v.48, #5-6)